Fiber Urine - NMR analysis
RM
May 13th Tue 2025
assume the LTR checks are done
## [1] 413##
## we have 413 samples in common
## and 5 samples in the experimental data that are not in metadata0.0.1 NMR spectra post processing
0.0.2 Step 1 Spectra calibration
Lets check the alanine doublets as it is
Lets see after calibration
0.0.3 Step 2 Remove the regions of the spectra that are not of interest
0.0.4 Step 3 Baseline correction
0.0.5 Step 4 Normalization
1 Analysis
1.1 PCA
##
## who are those PC3 outliers and why?## sampleID projectName cohortName sampleMatrixType tubeLabel sourceID
## 868 FIB00912 fibers C1 URI fib380-u1-t2 fib380
## 869 FIB00917 fibers C1 URI fib380-u1-t4 fib380
## 870 FIB00935 fibers C1 URI fib380-u1-t6 fib380
## 871 FIB00944 fibers C1 URI fib380-u1-t8 fib380
## 867 FIB00901 fibers C1 URI fib380-u1-t0 fib380
## sampleTimePoint visit timePoint type typeId
## 868 t2-u1 Clinic Visit 1 T2 Elephant Garlic V1
## 869 t4-u1 Clinic Visit 1 T4 Elephant Garlic V1
## 870 t6-u1 Clinic Visit 1 T6 Elephant Garlic V1
## 871 t8-u1 Clinic Visit 1 T8 Elephant Garlic V1
## 867 t0-u1 Clinic Visit 1 T0 Elephant Garlic V1
## sampleTimePoint key bmi age sex DOB height Weight
## 868 t2-v1 fib380t2-v1 22 34 Female 1989-01-07 167.5 60.6
## 869 t4-v1 fib380t4-v1 22 34 Female 1989-01-07 167.5 60.6
## 870 t6-v1 fib380t6-v1 22 34 Female 1989-01-07 167.5 60.6
## 871 t8-v1 fib380t8-v1 22 34 Female 1989-01-07 167.5 60.6
## 867 t0-v1 fib380t0-v1 22 34 Female 1989-01-07 167.5 60.6
## Screen Visit Date Screen Visit H2BT food date Clinic Visit Date
## 868 2023-11-02 6 2023-12-07 2023-12-07
## 869 2023-11-02 49 2023-12-07 2023-12-07
## 870 2023-11-02 27 2023-12-07 2023-12-07
## 871 2023-11-02 38 2023-12-07 2023-12-07
## 867 2023-11-02 2 2023-12-07 2023-12-07
## Clinic Visit H2BT Non standard Food Medication Activity
## 868 2 <NA> <NA> <NA>
## 869 2 <NA> <NA> <NA>
## 870 25 <NA> <NA> <NA>
## 871 49 <NA> <NA> <NA>
## 867 5 <NA> <NA> <NA>##
## PC3 outliers are from the same person: fib380 eating Elephant Garlic collected from 5 different timepoints
##
## From the loadings, it seems that those outliers are from high glucose in urine##
## Since this participant only participated in the Elephant Garlic study it may be wise to remove from the analysis
1.2 COMPASS
1.3 Visual Inspection using specOverlay
soutceID fib 380 (high glucose outlier) were omitted and only ploted at Timepoint T2, T4, T6, and T8
1.3.1 2,3-butanediol 1.125 ~ 1.150 –> Yacon
1.3.2 lactate 1.3 ~ 1.5 –> Apple at T2
1.3.3 s 1.92 –> Global Artichoke at T2? –> only two samples
1.3.4 s 2.045 –> Elephant Garlic peak at T4
1.3.5 s 3.1 –> Orange
1.3.6 s 3.3 –> Orange
